[BioC] interaction term contrast in Weaver mutant example of LIMMA manual
James W. MacDonald
jmacdon at med.umich.edu
Tue Sep 8 18:44:12 CEST 2009
Erika Melissari wrote:
> Dear bioconductor list,
> I am studing the Weaver experiment example of LIMMA manual and I am in a
> maze about the biological meaning of interaction term present among the
> I did not manage to understend what kind of differentially expressed gene
> this contrast takes-out.
In this experiment we can look at genes that change between the two time
points in the mutant samples, or that change between the two time points
in the wild type samples. In addition, we might be interested in those
genes that react differently in the two sample types. In other words, a
particular gene might increase expression in the wild type samples, but
actually decrease expression in the mutant samples.
This third comparison is known as an interaction.
> The interaction contrast is:
Correct. So using our example from above, the first term will be
negative (since the expression level went down in mutant samples). The
second term will be positive, since the expression went up over time in
the wild type samples, but since we subtract, we end up with a
(possibly) large negative number.
The same will be true of any scenario you can envision where the mutant
and wild type samples react differently to the incubation time. Another
example would be the situation where the mutant samples were
up-regulated at 21 hours, but the wild type samples were unaffected. In
this case you can see that we might have a large value for this contrast.
However, if both wild type and mutant samples were up-regulated
approximately the same amount, the resulting value would be very close
> The first bracket takes-out the differentially expressed genes between the
> mutant subjects at two different time points(21 and 11 minutes) and the
> second bracket those between the wild-type subject at the same different
> time points.
> ..but what differentially expressed genes takes-out the global interaction
> In order to evaluate an interaction do I need absolutely the four arrays
> in direct comparison done in this example?
Not four arrays, but four treatment/sample combinations. You will need
replication to compute this contrast.
> Thank you very much for any explaination
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James W. MacDonald, M.S.
University of Michigan
Department of Human Genetics
1241 E. Catherine St.
Ann Arbor MI 48109-5618
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